MODBASE, a database of annotated comparative protein structure models and associated resources.
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/).
Pieper
Ursula
U
Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
Eswar
Narayanan
N
Webb
Ben M
BM
Eramian
David
D
Kelly
Libusha
L
Barkan
David T
DT
Carter
Hannah
H
Mankoo
Parminder
P
Karchin
Rachel
R
Marti-Renom
Marc A
MA
Davis
Fred P
FP
Sali
Andrej
A
D030562:Databases, Protein; D023281:Genomics; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000235:genetics; D040681:Structural Homology, Protein; D014584:User-Computer Interface
D008024:Ligands; D011506:Proteins